Now that I'm back home and have access to my copy of Elbroch's Skulls book I've been looking over the skulls and figuring out what they are from. So far I believe I figured out the two here to genus at least, and know that there are at least two other species in the collection.
There are a lot of details visible in these pictures that can be used to figure out who the skull belonged to, but it would be difficult to go through very many of them. Instead, I will just go over a few of the main details I used. For reference the first skull in each pair is about 6.5 cm and the second skull is about 5 cm. Both are clearly rodents from the teeth, so I'll go from there.
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The first skull ended up being pretty easy for me to identify because of its size and the way the brain case sticks out squarely over the eye socket. Just flipping through the pictures of skulls I saw that it matched up with the muskrat (Ondatra zibethicus).
The second skull has a well developed post orbital process (the sharp protrusion over the eye socket). As far as I can tell, among rodents, those seem to mainly occur in the squirrel family.
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At first I thought the second skull might be a type of marmot because of the shape of the post orbital process (and because they are large members of the squirrel family). However when going through the details of the marmots things kept not seeming to match up quite right. What finally convinced me that it wasn't a marmot was that marmot skulls are pretty flat on top, somewhat similar to the muskrat skull, however this skull is fairly rounded. In hind sight the skull was smaller than the range given for marmots as well. With a little more searching, I found that ground squirrels (Spermophilus sps) fit the skull much better.
A couple of differences to note are the position of the zygomatic arch (the bone that forms the outer portion of the eye socket) and how curved (or straight) the incisors are. I don't know that these are more useful details to pay attention to than others, but they seem fairly easy to pay attention to.
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A couple of differences I notice on the ventral view are the size and shape of the palate, the relative position of the teeth (including parallel vs. angled) and the size and position of the incisive foramina (the narrow pair of holes behind the incisors).
I have not yet got down to species on the ground squirrel. There are a couple of different ground squirrel species in that region of Idaho that aren't in the skulls book and the skull doesn't seem to match up exactly with the ones that are.